annotateCTSS | R Documentation |
annotateCTSS
annotates the CTSS of a CAGEexp
object and computes
annotation statistics.
annotateConsensusClusters
annotates the consensus clusters
of a CAGEr object.
annotateCTSS(object, ranges, upstream = 500, downstream = 500)
## S4 method for signature 'CAGEexp,GRanges'
annotateCTSS(object, ranges, upstream = 500, downstream = 500)
annotateConsensusClusters(object, ranges, upstream = 500, downstream = 500)
## S4 method for signature 'CAGEexp,GRanges'
annotateConsensusClusters(object, ranges, upstream = 500, downstream = 500)
object |
|
ranges |
A |
upstream |
Number of bases upstream the start of the transcript models to be considered as part of the promoter region. |
downstream |
Number of bases downstream the start of the transcript models to be considered as part of the promoter region. |
annotateCTSS
returns the input object with the following
modifications:
The Genomic Ranges of the tagCountMatrix
experiment gains an
annotation
metadata column, with levels such as promoter
,
exon
, intron
and unknown
. If the annotation has a gene_name
metadata, then a genes
column is also added, with gene symbols from
the annotation.
The sample metadata gets new columns, indicating total counts in each of
the annotation levels. If the annotation has a gene_name
metadata, then
a genes
column is added to indicate the number of different gene symbols
detected.
annotateConsensusClusters
returns the input object with the same
modifications as above.
Charles Plessy
CTSStoGenes
, and the exampleZv9_annot
example data.
Other CAGEr object modifiers:
CTSStoGenes()
,
CustomConsensusClusters()
,
aggregateTagClusters()
,
clusterCTSS()
,
cumulativeCTSSdistribution()
,
getCTSS()
,
normalizeTagCount()
,
quantilePositions()
,
quickEnhancers()
,
resetCAGEexp()
,
summariseChrExpr()
Other CAGEr annotation functions:
plotAnnot()
,
ranges2annot()
,
ranges2genes()
,
ranges2names()
annotateCTSS(exampleCAGEexp, exampleZv9_annot)
colData(exampleCAGEexp)
annotateConsensusClusters(exampleCAGEexp, exampleZv9_annot)
consensusClustersGR(exampleCAGEexp)
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